Section by Section Description

FORCE_FIELD_SETTINGS

Key block (required)
This key block specifies various global options for the force field file, mostly concerned with the treatment of the non-bonded potentials.

ELSTAT_1-4_SCALE & VDW_1-4_SCALE

Most force fields scale the non-bonded interactions by a factor of 0.5 if the atoms are the terminal atoms of a defined torsion. This scaling factor, which is termed the 1-4 scaling factor, can also be different for the electrostatic potential and for the Van der Waals potentials and thus they are separately defined in the input.

VDW_DEFAULT_POTENTIAL

This keyword defines what kind of potential is used for the non-bonded van der Waals interactions. The potential types have been assigned integer values as defined in the following table.

VDW potential type		constants required (in order)
0	no potential	none
1	Lennard-Jones 12-6	Do, Ro
2	Exponential-6 or Buckingham	Do, Ro, x x=12.0 is standard
3	Purely Repulsive	Do, Ro, x
4	Purely Attractive (dispersion term)	Do, Ro

DIELECTRIC_CONSTANT

Default = 1.00
This defines the dielectric constant used for the calculation of the electrostatic interactions. For example, 1.00 = vacuum and 80 is that of bulk liquid water. Currently, only a constant dielectric has been implemented.

BONDS

Key block (required)
This key block specifies the potential type and parameters for each kind of MM bond stretching interaction. An example is given below.

BONDS
Atoms		pot	K	ro	NOTES
i - j		type	(kcal/molA^2)	(Ang)
=========================================
CA	CA	1	938.0	1.400	amber95
CT	CT	1	620.0	1.526	amber95
HC	Zr	0	0.0		no potential found
=========================================

The first two columns are the atom types (up to four characters long) and the third column is an integer specifying the potential type.

BOND potential type		constants required (in order)
0	no potential	none
1	simple harmonic: AMBER95, Sybyl	K, Ro

BENDS

Key block (required)
This key block specifies the potential type and parameters for each kind of MM bond angle interaction. An example is given below.

The first three columns specify the atom types and the fourth column is an integer specifying the potential type. The angle bend potential types are described in the table below with the additional constants required.

BEND potential type		constants required (in order)
0	no potential	none
1	theta harmonic: AMBER95, SYBYL	K,qo (q in degrees)

Notice that wild cards can be specified for both terminal positions of the bend or just one as in the example above. It is important that the parameters be ordered from the least specific (those containing the most wild cards) to the most specific parameters.

TORSIONS

Key block (required)
This key block specifies the potential type and parameters for each kind of MM bond torsion interaction. For the bond stretching and bending potentials, only one potential has to date been implemented since both AMBER and SYBYL both use simple harmonic potentials. However, AMBER and SYBYL use different functional forms to represent the torsion potentials, each with their own set of parameters. The AMBER and SYBYL torsional potentials used in this program are defined in the table below.

TORSION potential type		constants required (in order)
0	no potential	none
1	AMBER:	Ki, ni (periodicity-integer), fo,i (phase shift)
2	SYBYL:	K, s

Notice that the two potentials have a different number of parameters. For example, when the program reads 'potential type' number 1, it will expect three parameters K_i, n_i, f_o,i. Further notice that the AMBER torsional potential is a sum of Fourier components (this is what the index i refers to).

Below is an example of the TORSIONS key block, made up of AMBER force field types.

Most AMBER torsion potentials are not specific to all four atoms i-j-k-l, but only on the central two, j-k. Wild cards are specified with the '*' symbol as illustrated above. Again, the ordering is important. The parameters should be ordered from least specific (those containing the most wild cards) to most specific. The AMBER torsion potential can be composed of more than one Fourier component for a single torsion potential. Additional Fourier components are specified with the '&' continuation symbol as in the example above. At the moment, up to 6 Fourier components are allowed. Notice that the individual components need not be specified in any particular order. In the above example key block, there are only 5 torsional potentials defined, not 8. Two of the potentials are composed of more than one Fourier component as indicated by the '&' continuation line.

Below is an example of the TORSIONS key block for the SYBYL force field. Notice that the potential types are all '2'. There are fewer parameters and no multi component potentials. Also, some potentials are defined with two or only one wild card.

One can also mix different potential types within the same force field file, as illustrated below. In this example, three are three potentials. The first two are SYBYL type potentials whereas the last one is a multi component AMBER potential.

OUT-OF_PLANE

Key block (required)
This key block specifies the potential type and parameters for each kind of MM out of plane bend. This potential is sometimes referred to as the inversion potential or improper torsions (depending on the force field). The potential types currently supported are provided in the table below.

out-of-plane potential type	description	constants required (in order)
0	no potential	none
1	AMBER:	K, n, fo (n=2, fo = 180° for planar, n=3, fo = 120° for tetrahedral)
2	SYBYL: d is the distance of the plane in Ang.	K

An example of the key block for the AMBER type potentials is given below. It is important to realize that the atom k is the atom k is the central atom. (We have adopted the somewhat odd standard of AMBER in this respect).

VAN DER WAALS

Key block (required)
This key block specifies the potential type and parameters for each kind of MM van der Waals interaction between two atoms. A sample key block is shown below:

The van der Waals key block is somewhat different than the previous key blocks, because generally not every atom pair is defined with its own parameters. Rather, the parameters are assigned on a per atom basis and then special combination rules are used to construct the parameters for each atom pair combination. For this reason, a default potential type is defined in the FORCE_FIELD_SETTINGS key block.

VDW potential type		constants required (in order)
0	no potential	none
1	Lennard-Jones 12-6	Do, Ro
2	Exponential-6 or Buckingham	Do, Ro, x x=12.0 is standard
3	Purely Repulsive	Do, Ro, x

For each type of van der Waals interaction, the program first scans the key block for pair specific parameters. For pair specific potentials, the default potential type can be replaced by any of the available potentials. The three sample lines below specify pair-specific potentials. The two atom types must be separated by a hyphen with spaces between the hyphen and the atom type. Following the specification of the atom pair, the potential type is defined. If D or d is specified here, then this means to use the default potential type. Following the potential type are the parameters needed for that potential type (see above table).

If a pair specific parameter can't be found, then the program looks for individual atom parameters corresponding to each of the atom types in the pair. The pair specific parameters are then constructed from combination of the two individual atom parameters using the following combination rules:

When individual atom parameters are not used, no potential type is specified since the default potential type is always used. An example is given below.

The ability to define pair specific parameters is especially useful for those force fields that have different combination rules than used in the program. For example, Jorgensen's TIP3P water force field uses geometric averages for both D_ij and R_ij.

MASSES & ATOM LABELS

Key block (required)
This key block specifies the default masses for each MM atom type and the element label for each MM atom type. In an ADF QM/MM run, the element label defined for each atom type is the label used for printing out to the LOGFILE. This allows one to easily cut and paste the generated coordinates to a molecule viewing program without having to go in and changing all of the "CT"s to "C"s.

A sample key block is shown below:

The first column is the MM atom type, the second is the label used for printing and the third column is the mass of the atom type. The atoms do not have to be specified in any particular order.

CHARGES

Key block (optional)
This key block specifies the parameters for the charges on the atoms by atom type. To date only the initial charge is available, however if some sort of charge equilibration scheme was introduced the parameters would go here. NOTE: initial charges can also be specified on a per atom basis in the MM INPUT file.